[HTML][HTML] Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code
L López-Villellas, CCK Mikkelsen… - Computer Physics …, 2023 - Elsevier
In molecular dynamics simulations we can often increase the time step by imposing
constraints on bond lengths and bond angles. This allows us to extend the length of the time …
constraints on bond lengths and bond angles. This allows us to extend the length of the time …
[HTML][HTML] Computation of quasiseparable representations of Green matrices
P Boito, Y Eidelman - Linear Algebra and its Applications, 2024 - Elsevier
The well-known Asplund theorem states that the inverse of a (possibly one-sided) band
matrix A is a Green matrix. In accordance with quasiseparable theory, such a matrix admits a …
matrix A is a Green matrix. In accordance with quasiseparable theory, such a matrix admits a …
A survey of the parallel performance and accuracy of Poisson solvers for electronic structure calculations
P García‐Risueño, J Alberdi‐Rodriguez… - Journal of …, 2014 - Wiley Online Library
We present an analysis of different methods to calculate the classical electrostatic Hartree
potential created by charge distributions. Our goal is to provide the reader with an estimation …
potential created by charge distributions. Our goal is to provide the reader with an estimation …
Accurate and efficient constrained molecular dynamics of polymers through Newton's method and special purpose code
In molecular dynamics simulations we can often increase the time step by imposing
constraints on internal degrees of freedom, such as bond lengths and bond angles. This …
constraints on internal degrees of freedom, such as bond lengths and bond angles. This …
Exact and efficient calculation of Lagrange multipliers in constrained biological polymers: Proteins and nucleic acids as example cases
P García-Risueño, P Echenique, JL Alonso - arXiv preprint arXiv …, 2011 - arxiv.org
In order to accelerate molecular dynamics simulations, it is very common to impose
holonomic constraints on their hardest degrees of freedom. In this way, the time step used to …
holonomic constraints on their hardest degrees of freedom. In this way, the time step used to …
Partial differential equations constrained combinatorial optimization on an adiabatic quantum computer
R Chandra - 2013 - search.proquest.com
Partial differential equation-constrained combinatorial optimization (PDECCO) problems are
a mixture of continuous and discrete optimization problems. PDECCO problems have …
a mixture of continuous and discrete optimization problems. PDECCO problems have …
Exact and efficient calculation of the derivatives of Lagrange multipliers for molecular dynamics simulations of biological molecules and polymers
P García-Risueño - Physica Scripta, 2019 - iopscience.iop.org
In the simulation of biological molecules and polymers, it is customary to impose constraints
on the fastest degrees of freedom so as to freeze their motion and increase the time step. An …
on the fastest degrees of freedom so as to freeze their motion and increase the time step. An …